Source code for morphforge.simulation.neuron.objects.obj_basesetup
#!/usr/bin/python
# -*- coding: utf-8 -*-
# ---------------------------------------------------------------------
# Copyright (c) 2012 Michael Hull.
# All rights reserved.
#
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# modification, are permitted provided that the following conditions
# are met:
#
# - Redistributions of source code must retain the above copyright
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# - Redistributions in binary form must reproduce the above copyright
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# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
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# ----------------------------------------------------------------------
from morphforge.simulation.neuron.objects.neuronobject import NEURONObject
from morphforge.simulation.neuron.simulationdatacontainers import MHOCSections
[docs]class NeuronSimSetupObj(NEURONObject):
[docs] def __init__(self, simsettings, simulation):
super(NeuronSimSetupObj, self).__init__(
name='mneuronbasesetup',
simulation=simulation)
self.simsettings = simsettings
[docs] def build_hoc(self, hocfile_obj):
hocfile_obj.add_to_section(MHOCSections.InitHeader, """load_file("noload.hoc")""")
if self.simsettings['cvode']:
hocfile_obj.add_to_section( MHOCSections.InitHeader, """cvode_active(1)""")
else:
hocfile_obj.add_to_section( MHOCSections.InitHeader, """cvode_active(0)""")
hocfile_obj.add_to_section(MHOCSections.InitSimParams, """dt=%s"""%(self.simsettings["dt"].rescale("ms").magnitude))
# Simulator accuracy:
hocfile_obj.add_to_section( MHOCSections.InitHeader, """cvode.atol(%e)""" % self.simsettings['abstol'])
hocfile_obj.add_to_section( MHOCSections.InitHeader, """cvode.rtol(%e)""" % self.simsettings['reltol'])
# Duration of the simulation:
hocfile_obj.add_to_section(MHOCSections.InitSimParams, """tstop=%s"""%(self.simsettings["tstop"].rescale("ms").magnitude))
hocfile_obj.add_to_section(MHOCSections.InitRecords, "\n".join(["objref rect", "rect = new Vector()", "rect.record(&t)"]))
[docs] def build_mod(self, modfile_set):
pass
[docs] def get_recordable(self, what, **kwargs):
raise NotImplementedError()